Shashank Manohar, the BCCI president, said Mansur Ali Khan Pataudi, Sunil Gavaskar and Ravi Shastri - former national captains and members of the tournament's governing council - will decide how to organise future versions of the IPL following the scandal.
A statement from the BCCI said the allegations against Modi had "brought a bad name to the administration of cricket and the game itself".
He now has 15 days to show why disciplinary action should not be taken against him.
Modi has been a key figure in building the IPL from its launch in 2008 into a multi-billion-dollar commercial juggernaut followed by millions of fans in India and beyond.
Market analysts currently put the tournament's brand value at more than $4bn, well in excess of more long-running sports brands such as English football team Manchester United.
Gideon Haigh, a cricket writer based in Melbourne, Australia, told Al Jazeera that the preconditions of scandal and corruption have always existed within the competition which has untransparent accounts and poor regulation.
Haigh said transparency within the IPL was impossible from its inception because of its adoption of a private ownership model.
"The reason they call it that is because it's private. You might not like that but it is the way of business," he said.
The seeds of the current crisis originate in a Twitter post by Modi two weeks ago when he revealed the ownership details of a new franchise set to join the glitzy and globally popular IPL in 2011.
In the posting, he embarrassed a high-profile member of the government, Shashi Tharoor, a junior foreign minister, by claiming his girlfriend had been given a free stake in the new team.
The revelation ultimately forced Tharoor to resign from the government amid opposition accusations that he had been misusing his office for personal benefit.
Since then, the Indian finance ministry has launched a wide-ranging tax inquiry into the IPL, the BCCI and the owners of its teams, including powerful business leaders and stars in the Bollywood film industry.
|Tharoor resigned amid controversy over ownership of a new IPL team [AFP]
Many are blaming Modi for bringing the tax man to their door.
Indian newspapers and TV news networks have been reporting several as yet unproven allegations over Modi's unpaid tax liabilities, general corruption and kickbacks, and even possible match-fixing.
The latter is seen as a particularly serious offence in India after a 2000 scandal revealed widespread illegal betting and corruption by Indian bookmakers and some leading players.
Narayanan Madhavan, an editor at the Hindustan Times newspaper, said told Al Jazeera from New Delhi: "The crisis here is not about the IPL, the cricket or the fans. It is about the administration and the corruption there.
"The administrators have been horribly unaccountable in this whole game. What we need now are administrators of integrity and credibility - that is where the action should shift next."
Modi had been defiant in recent days, dismissing calls to step down despite losing the support of several of his colleagues and pressure from the government.
"People pressurising me to resign - I can tell you will not happen. Let them remove me then," he posted on Twitter on Saturday.
"Wait for the IPL to finish - I will reveal the men who have tried to bring disrepute to the game and how we stopped them from doing it."
Haigh said Modi's contribution to the tournament could not be overstated.
"If Modi is history, in a sense it will be a great shame because he does represent a genuine entrepreneur in a sport that has been run chiefly by administrators and managers."
"He has brought vision and a common touch to cricket ... because he comes from outside cricket's traditional bureaucratic circles.
"I think senior politicians and administrators are more culpable - alleged wise heads who pandered to Modi's ego and ambition because it suited their particular purposes."